Well... the scientists have studied quite a lot concerning the nature of Eywa, and its abilities. I'd go with a former theory of Grace's body being kept alive. You know, just in case.

Sure, to most everyone's knowledge, Grace can't return in her Avatar. But since the RDA is gone, what's the purpose of some of the other scientists-as-avatars staying on Pandora? There's really nothing for them to do except to discover more things. Keeping Grace's avatar alive wouldn't be much of a problem for them.

My idea is, maybe Grace has taken a much longer period to "pass through the eye of Eywa". In other words, since Grace was weak at the time of transfer, maybe it just takes a longer time to transfer "badly-damaged information".

There may be a point in the sequel where Jake starts thinking about this very same concept, takes Grace's vegetative avatar to the Tree of Souls again, makes a tsaheylu with one of the roots of the tree, and uses all his strength and effort to try and find Grace while passing through the eye of Eywa himself to bring her back to her avatar. He's logically the only one on Pandora who has a chance of surviving this, since he's done it before.

This concept reminds me very much of Dune, how Muad'dib became the powerful one he was ultimately destined to be by putting himself directly into the Bene Gesserit's trance, and traveling to "the place they cannot go".

Perhaps Jake will attempt this very act: trying to bring Grace back, succeeding, and in the process, becoming more powerful than anyone had imagined before, perhaps wielding the ability to... dare I say it... more or less control the will of Eywa. Or maybe not. Maybe he'll have a special connection with Eywa that no other Na'vi soul possesses. Perhaps he will become their prophet; the Na'vi's "chosen one".

Now that is a really interesting concept - I like it. After all, if grace's memories are in the network, it would still be possible to separate/copy them to the body at a later time - possibly, her injury means they because more diffuse and have spread out through the network, which is why they did not transfer to her avatar, but they could still be reintegrated in that case.